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Situs on Biowulf & Helix

Situs is a package for the modeling of atomic resolution structures into low-resolution density maps e.g. from electron microscopy, tomography, or small angle X-ray scattering.

Situs website

Situs is a single-threaded application and cannot use multiple processors on a node.

On Helix

Use module load situs to set up your environment for Situs, and then type any Situs command.

Batch Job On Biowulf

Create a batch script containing the Situs commands, along the following lines:

--------- /data/username/myrun ------------
#!/bin/bash -v

module load situs
cd /data/username/situs
map2map 0_mt.ascii 1_mt.situs
voldiff 1_nm.situs 1_mt.situs 2_s1.situs
volhist 3_nm.situs test
qrange 4_s1.situs 0_ncd.pdb
---------------- end of script -------------

Submit this job with sbatch

sbatch  myrun

Examination of structures via VMD is best performed on Helix or on the Biowulf login node, which is intended for interactive use. Open an Xwindows session and start up VMD. Warning: if your VMD session becomes excessively cpu or memory-intensive on the Biowulf login node, it may be automatically killed.

Interactive job on Biowulf

Allocate an interactive session with sinteractive, load the Situs module, and then run any Situs command. Sample session:

[user@biowulf ~]$ sinteractive
salloc.exe: Granted job allocation 1340957
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0032 are ready for job

[user@cn0032 ~]$ module load situs

[user@cn0032 ~]$ map2map 0_mt.ascii 1_mt.situs
[...]

[user@cn0032 ~]$ exit
exit
salloc.exe: Relinquishing job allocation 1340957
salloc.exe: Job allocation 1340957 has been revoked.

Documentation

Situs User Guide